Environmental DNA (eDNA) metabarcoding provides a non-invasive tool for monitoring marine biodiversity in complex ecosystems. In this study, we applied eDNA techniques to investigate the spatiotemporal dynamics of fish communities in Daya Bay, South China Sea, by analyzing 120 water column and 113 sediment samples collected across four seasons. Our research aimed to characterize the seasonal turnover and habitat-specific partitioning of fish community structures. The results revealed that sediment matrices exhibited significantly higher alpha diversity compared to water samples. However, sediment showed lower community heterogeneity-quantified as within-group Bray-Curtis dispersion-particularly during the warm seasons (spring and summer) compared with the water column. Conversely, during the cold seasons (autumn and winter), sediment matrices showed lower alpha diversity but higher community heterogeneity. Using LEfSe and random forest models, we identified a suite of discriminative indicator taxa that characterized these community shifts. Based on relative read abundance (RRA), Johnius and Pennahia were significantly enriched in the water column, while Cynoglossus and Zebrias were primarily associated with sediment habitats. These findings highlight the complementary roles of water and sediment eDNA in capturing the full spectrum of fish biodiversity. While this study primarily describes observed patterns within a dynamic hydrographic context, it provides foundational data for advancing eDNA-based biomonitoring in subtropical marine ecosystems and supports the development of targeted conservation strategies.

Spawning habitats are critical for population persistence, yet they remain poorly resolved for many endangered and data-poor marine species. Developing effective and non-invasive approaches to identify these habitats is therefore essential for conservation and management. Here, we integrated bottom trawl surveys with environmental DNA (eDNA) metabarcoding and droplet digital PCR (ddPCR) to investigate the spawning-season distribution of an endangered marine fish, the large yellow croaker (Larimichthys crocea), in the South China Sea. Reproductive activity was suggested during autumn, with a potential aggregation hotspot identified in a narrow depth range (20–41 m), whereas no clear spawning signals were observed during the sampled spring period. This pattern suggests a seasonally aggregated potential spawning habitat, potentially associated with local hydrodynamic conditions. Across methods, eDNA approaches showed higher detection sensitivity than conventional trawl surveys, while ddPCR provided clearer spatial differentiation than metabarcoding. The consistency between molecular and fishery data suggests that eDNA captures major spatial patterns and indicates additional potential distribution areas beyond those detected by trawl surveys. Our results demonstrate that integrating eDNA with traditional surveys improves the reliability of habitat identification, while providing a practical, non-invasive approach for delineating potential critical habitats. This approach supports habitat-based management of endangered marine species, particularly where direct observation or destructive sampling is limited.

The marine biological carbon pump is a key process in the global carbon cycle, with mesopelagic fish playing a crucial role by facilitating the transport of organic carbon from surface waters to the deep ocean through diel vertical migration (DVM). This process enhances carbon sequestration in mid-depth waters and influences carbon flux at the air-sea interface. Despite their significant biomass, the contribution of mesopelagic fish to carbon export fluxes remains poorly quantified at both global and regional scales. This review synthesizes current research on carbon export mediated by mesopelagic fish DVM, focusing on relevant carbon fluxes in the open ocean and deep regions of marginal seas (e.g., basins, continental slopes, and canyon systems) where mesopelagic fish are known to occur. The review discusses the methods used to quantify these fluxes, the associated challenges, and the implications for global carbon cycling. Finally, the review proposes future research directions to improve our understanding of the role of mesopelagic fish in marine ecosystems and their impact on ocean carbon dynamics in the context of climate change.

Mesopelagic fish are important components of pelagic food webs and contributors to the redistribution of organic matter through diel vertical migration. However, mesopelagic fish communities are often treated as functionally similar groups in ecosystem and biogeochemical studies, despite potential differences in feeding ecology among species. We examined the feeding ecology of two sympatric myctophids, Bolinichthys longipes and Ceratoscopelus warmingii, in the deep scattering layer of the Xisha area, South China Sea, using stomach content analysis combined with trophic niche metrics, diel feeding patterns, and daily ration estimates. Despite co-occurrence at similar depths and trophic levels, both species differed consistently in prey utilization and feeding schedules. Ceratoscopelus warmingii consumed a broad range of prey, including amphipods and euphausiids, whereas B. longipes fed predominantly on copepods. Biomass-based niche metrics indicated separation in dietary contribution of prey, and size-related dietary variation was evident in C. warmingii but limited in B. longipes. Feeding periodicity also contrasted between species: C. warmingii showed a stronger nocturnal increase in stomach fullness, while B. longipes showed no clear diel peak. Daily ration estimates indicated substantial ingestion in both species, but the timing of feeding relative to vertical migration differed. These results suggest that co-occurring mesopelagic fish may interact with different components of the pelagic food web and differ in the coupling between feeding and vertical migration. Recognizing trophic heterogeneity within mesopelagic communities may improve representation of these assemblages in ecosystem and biogeochemical frameworks.

Mesopelagic fishes are important components of pelagic food webs and contributors to the redistribution of organic matter through diel vertical migration, yet their ecological roles are often represented using functionally homogeneous assumptions. We examined the feeding ecology of two sympatric myctophids, Bolinichthys longipes and Ceratoscopelus warmingii, in the deep scattering layer of the Xisha area, South China Sea, using stomach content analysis combined with trophic niche metrics, diel feeding patterns, and daily ration estimates. Despite co-occurrence at similar depths and trophic levels, the species differed consistently in prey utilization and feeding schedules. C. warmingii incorporated a broader range of prey categories, whereas B. longipes fed predominantly on copepods. Biomass-based niche metrics indicated separation in dietary contribution of prey, and ontogenetic dietary shifts were evident in C. warmingii but limited in B. longipes. Feeding periodicity also contrasted between species: C. warmingii showed a distinct nocturnal feeding peak, while B. longipes fed more continuously. Daily ration estimates indicated substantial ingestion in both species, but the timing of feeding relative to vertical migration differed. These results suggest that co-occurring mesopelagic fishes may interact with different components of the pelagic food web and differ in the coupling between feeding and vertical migration. Consequently, species-level trophic behavior may influence pathways by which surface-derived organic matter is processed and redistributed in the ocean interior. Recognizing trophic heterogeneity within mesopelagic communities may improve representation of these assemblages in ecosystem and biogeochemical frameworks.

Marine fisheries increasingly operate under conditions that constrain conventional biodiversity monitoring, particularly in observationally constrained environments. Nocturnal light-fishing represents a widespread anthropogenic pressure in such regions, yet its ecological effects on marine vertebrate assemblages remain insufficiently documented. Here, we assess changes in cetacean and fish assemblages associated with light falling-net fisheries by integrating environmental DNA (eDNA) metabarcoding with visual observations and net sampling in the Dongsha waters of the South China Sea. Field surveys were conducted aboard active light falling-net fishing vessels, with eDNA samples collected before and after artificial illumination. Across all methods, 14 cetacean species and 221 fish species were detected. eDNA consistently revealed higher species diversity than conventional approaches. Following illumination, eDNA detections indicated increased cetacean occurrence and fish diversity. Cetacean species count increased from 8 to 12, and fish species count from 121 to 206, together with higher relative read abundance, supporting an aggregating effect of artificial light on marine vertebrates. Local optimization of cetacean primers further enhanced detection sensitivity. Overall, our findings demonstrate that eDNA analysis provides an effective and practical tool for detecting fisheries-associated changes in marine vertebrate assemblages, offering field-based environmental evidence to support the assessment of anthropogenic pressures in data-poor tropical marine ecosystems.

Simplified cylindrical twine models were widely adopted to reduce computational cost in CFD simulation of fishing nets, but they ignored woven microstructures and induced systematic hydrodynamic prediction errors. This study established three identical-solidity net models (cylindrical, twisted, warp-knitted) and conducted k-ω SST simulations at Reynolds number (Re) =1800 and angles of attack (AOAs) from 0° to 90°. Results revealed drag coefficients followed the order warp-knitted > twisted > cylindrical; at 90° AOA, cylindrical net underpredicted drag by 5.20% and 11.71% compared with twisted and warp-knitted nets, respectively. All nets produced single-peak lift curves with maximum values at 45°. The high-fidelity woven models achieved 89.2%–99.1% prediction accuracy to real net, while cylindrical models only reached 80%–87.4%. Helical grooves and interlaced interstices aggravated boundary layer separation and small-scale vortices, which smooth cylindrical twines failed to reproduce. Pressure drag dominated total drag force, and mesh knot cross-sections generated the largest flow-field discrepancies. Root mean square error (RMSE), mean bias error (MBE), and relative error (RE) were applied to quantitatively separated pressure and frictional drag deviations. Hierarchical simulation schemes and linear correction formulas were proposed to balance computational accuracy and cost for the design of aquaculture cages and fishing gear.

Golden pompano (Trachinotus ovatus) ranks among the most commercially important and high-yield marine finfish species in Chinese mariculture. In response to the requirement for monitoring fish in aquaculture, this study employed Adaptive Resolution Imaging Sonar (ARIS) to observe the body length, swimming speed, and spatial distribution of untreated (GI group), anesthetized (GII group), and injured (GIII group) T. ovatus in a small offshore cage (1.5 × 1.5 × 2.5 m3). The results demonstrated that the relative error range of the length measurement of the T. ovatus spanned from −3.24 to 4.35, and there was no significant difference between the observed and actual body lengths (ANOVA, p > 0.05). We failed to detect a significant difference in the average speed between the untreated group and the anesthetized group (ANOVA, p > 0.05; Tukey’s HSD, p > 0.05). The injured fish exhibited a significantly lower swimming speed compared to untreated and anesthetized individuals (ANOVA, p < 0.01; Tukey’s HSD, p < 0.01). Untreated individuals and fish with physical injuries exhibited mean vertical distribution depths of 1.06 ± 0.47 m and 1.70 ± 0.51 m, respectively, with the injured fish occupying a significantly greater water depth than the untreated conspecifics (one-way ANOVA, p < 0.01). There was a highly significant association between the treatment status of the fish (untreated/injured) and the frequency of water layer distribution (χ2(2) = 196.78, p < 0.01). The findings of the present study can furnish specific methodological references for the imaging sonar-based monitoring of T. ovatus within aquaculture cage systems. Nevertheless, the study is subject to several inherent limitations, including a small sample size for the injured group (n = 3), the employment of an artificial injury model, and the confinement of experimental subjects to a closed cage environment; these factors may introduce statistical uncertainty and thus exert a considerable impact on the external validity of the study’s results.

In the summer of 2019, an investigation was conducted using data obtained from a fishery hauls survey to analyze the influence of a dipole eddy on the fish community within the West-central South China Sea (WC_SCS). This dipole eddy consisted of a cyclonic eddy (CE) and an anticyclonic eddy (AE) that coexisted in the study area during the survey. A total of 8381 individual fish were captured, with 1241 found in the AE, 329 in the CE, and 6811 in the dipole frontal zone. The predominant fish families observed were Scombridae, Nomeidae, and Carangidae, which collectively represented over 97% in the AE, 21% in the CE, and 98% in the frontal zone. While ten species were present in the two dipole eddies and the associated front, one species was exclusive to the AE, two species were exclusive to the CE, and seven species were exclusive to the frontal zone. Notably, there were significant disparities in fish abundance among the AE, CE, and frontal zone, with average abundances of 177, 54, and 1,703 ind/2h, respectively. Abundance levels ranged from 7 to 3119 ind/2h, with the highest concentrations observed in the frontal zone, and relatively high abundance was also noted in the core of the AE and in the transition zone between the AE core and the dipole front. Through cluster analysis, three distinct fish groups (A, B, and C) were identified. Groups A and C correspond to the CE and AE edges, while group B aligns with the AE core, the front zone, and the transition zone between the AE core and the front. Within the study area, fish abundance exhibited a negative correlation with sea surface currents in the longitudinal direction. However, in the region characterized by weak currents, referred to as group B, which displayed the highest fish abundance, the fish population demonstrated a positive correlation with sea surface chlorophyll-a concentration. Despite the three moonless stations among the four located in the frontal zone having a higher abundance compared to the remaining moonlit station, these four stations are grouped together in the results of the cluster analysis. These findings highlight the significant impact of the dipole eddy on the structure and distribution of fish communities in the WC_SCS.

Cold seeps, unique deep-sea ecosystems driven by hydrocarbon- and sulfide-rich fluid fluxes, support mesopelagic fish communities. Fish gut microbiota are vital to host metabolism and health, and interact closely with the surrounding water environment. However, information on gut bacterial composition and potential functional profiles of mesopelagic fishes in the cold seep has rarely been explored. In this study, high-throughput sequencing of the 16S rRNA gene was used to compare gut microbiota of mesopelagic fishes collected from the cold seep environment (Bolinichthys longipes, Ceratoscopelus warmingii) and mesopelagic fishes from non-cold seep environment (B. longipes, Diaphus brachycephalus, Diaphus signatus). Significant differences were found in gut bacterial composition and predicted functional profiles between the two distinct fish habitats. Within B. longipes, clear differences in gut bacterial composition were detected between cold seep and non-cold seep populations, suggesting a potential habitat-associated effect. The genera Blastopirellula, Ruegeria, and Rubripirellula, which are known to be involved in sulfide and hydrocarbon transformations, were significantly more abundant in cold seep fish (p < 0.05). In contrast, Acinetobacter was significantly enriched in fish outside the cold seep (p < 0.05). The differences in gut bacterial composition between the two habitats were primarily driven by the “abundant” subcommunities. Co-occurrence network analysis revealed more complex gut microbiome networks in cold seep fishes. Functional predictions using FAPROTAX showed that the gut microbiome associated with cold seep fish harbored higher predicted functional potential related to methane-, nitrogen-, and sulfur-associated processes. Meanwhile, PICRUSt2 analyses indicated a higher representation of predicted pathways associated with lipid metabolism and hydrocarbon degradation under cold seep conditions. Together, these results suggest that the cold seep environment may influence the structure and predicted functional potential of mesopelagic fish gut microbiota.

Mesopelagic fish represent the largest vertebrate biomass on Earth, yet quantifying their role in marine carbon fluxes and the marine environment remains a challenge. Here, we present a mechanistic model integrating body size- and temperature-dependent daily carbon release processes to estimate dissolved organic carbon (DOC), carbon dioxide (CO2), and particulate carbon (PC) released by mesopelagic fish across the global open ocean. Carbon budgets were modeled separately for diel vertically migratory (DVM) and non-vertically migratory (NM) mesopelagic fish in tropical/subtropical (40°N-40°S) and high-latitude (40°-70°N/S) zones. Our results indicate that mesopelagic fish release 0.64-8.29, 0.48-6.17, and 0.18-2.30 Pg C/yr of DOC, CO2, and PC, respectively, with a net production of 0.16-2.20 Pg C/yr. DVM fish mediate an active carbon export of 0.23-3.85 Pg C/yr through vertical migration, which is comparable to the active carbon fluxes mediated by mesozooplankton. Our results also show that the gross growth efficiency (i.e., net production divided by ingested food carbon, 12%) of DVM mesopelagic fish is, on average 21% higher than that of NM mesopelagic fish on a global scale, which provides a new explanation for the advantages of diel vertical migration. These findings provide the first global estimates of mesopelagic fish-driven DOC, CO2, and PC fluxes, highlighting their important role in the ocean carbon cycle, biological carbon pump, and marine environment.

The selection of environmental variables with different spatial resolutions is a critical factor affecting the accuracy of machine learning-based fishery forecasting. In this study, spring-season survey data of Decapterus macarellus in the South China Sea from 2016 to 2024 were used to construct six machine learning models—decision tree (DT), extra trees (ETs), K-Nearest Neighbors (KNN), light gradient boosting machine (LGBM), random forest (RF), and extreme gradient boosting (XGB)—based on seven environmental variables (e.g., sea surface temperature (SST), chlorophyll-a concentration (CHL)) at four spatial resolutions (0.083°, 0.25°, 0.5°, and 1°), filtered using Pearson correlation analysis. Optimal models were selected under each resolution through performance comparison. SHapley Additive exPlanations (SHAP) values were employed to interpret the contribution of environmental predictors, and the maximum entropy (MaxEnt) model was used to perform habitat suitability mapping. Results showed that the XGB model at 0.083° resolution achieved the best performance, with the area under the receiver operating characteristic curve (ROC_AUC) = 0.836, accuracy = 0.793, and negative predictive value = 0.862, outperforming models at coarser resolutions. CHL was identified as the most influential variable, showing high importance in both the SHAP distribution and the cumulative area under the curve contribution. Predicted suitable habitats were mainly located in the northern and central-southern South China Sea, with the latter covering a broader area. This study is the first to systematically evaluate the impact of spatial resolution on environmental variable selection in machine learning models, integrating SHAP-based interpretability with MaxEnt modeling to achieve reliable habitat suitability prediction, offering valuable insights for fishery forecasting in the South China Sea.

Based on bottom-trawl survey data collected in 2006–2020 in the Beibu Gulf of the South China Sea (SCS), we developed and calibrated a multispecies size-spectrum model for the coastal fishery ecosystem. We summarized the national official statistical data on domestic marine fisheries in the SCS based on the fishery statistical yearbooks of China and Vietnam. The real fishing effort of the neritic fishery in the SCS was evaluated by a comprehensive weighted score verify the accuracy of the model output results. The size spectrum of the marine fishery community in the BBG has been declining over the past 15 years. The community has adapted to external disturbances to some degree, but there have been significant changes in its internal structure: the proportion of most species groups has become more even, the average trophic level has decreased, and many species have experienced individual body-size miniaturization. By comparing the simulated relative fishing effort with the calculated real fishing effort over time, the decline of BBG fishery stocks was shown to be mainly attributed to the increasing fishing pressure, while frequent climate events may affect the size or quality of the habitable environment, thereby disrupted the recovery of the community. Our data suggest that small community sizes and changed community structure caused by overfishing may weaken the resilience of the community to climate anomalies. The design of coastal fishery management in the BBG should dynamically adjust fishery-management strategies taking into account the status of the community and impacts of climate anomalies.

Understanding the feeding mechanisms and interspecific coexistence of sharks is crucial for effective conservation. This study conducted stable isotope analysis on muscle and liver samples from 449 individuals of eight common bycatch shark species collected via bottom trawling in the northern South China Sea (NSCS). Results revealed significant differences in δ13C and δ15N values among species and tissue types. Scoliodon laticaudus exhibited the highest trophic position (TPmuscle = 4.60 ± 0.33; TPliver = 4.53 ± 0.29), while Apristurus platyrhynchus had the lowest (TPmuscle = 2.97 ± 0.44; TPliver = 2.75 ± 0.53). Muscle and liver isotopic signals were consistent, but δ13C differences indicated distinct carbon sources, with Carcharhinus sorrah linked to deep-sea organic matter and S. laticaudus to coastal inputs. Significant correlations between δ13C/δ15N and body length in A. platyrhynchus and Cephaloscyllium fasciatum suggest ontogenetic shifts in diet and habitat toward deeper waters. Trophic niche analysis using corrected standard ellipse area (SEAc) showed Halaelurus burgeri with the widest trophic niche (SEAc > 1.7‰2), reflecting a broad diet, while C. fasciatum had the narrowest (SEAc < 0.3‰2), indicating specialized feeding. Additionally, H. burgeri and C. sarawakensis exhibited significant niche differentiation, reducing interspecific competition, whereas C. fasciatum and Squalus megalops showed high niche overlap, suggesting intense resource competition. The narrower liver niche of C. sarawakensis may reflect recent habitat constriction due to bottom trawling. This study elucidates the feeding ecology and habitat resource utilization of NSCS sharks, providing a scientific basis for effective conservation strategies for shark populations in the region.

China is the largest producer of marine capture fisheries globally. Overfishing since the 1970s has led to a decline in fishery resources in Chinese coastal waters. After China’s reform and opening up, a series of management measures were implemented to alleviate marine fishing pressure and conserve the fisheries resources. We conducted a comprehensive assessment for multispecies fisheries in the South China Sea (SCS) to explore whether fisheries management has been effective in recovery of the resources. Indicators of the exploitation status of major commercial fish species were assessed using statistical catch data and survey data simultaneously. The results reveal a significant shift in bottom-trawl fishery, with its share of the total catch transitioning from an upward to a currently downward trend. The species composition of bottom-trawl fisheries has undergone substantial changes in the SCS over six decades. Stock assessment results based on catch data indicated some positive signals, with small pelagic fishes, such as herrings, anchovies, mackerel and scad recovering from overfished/overfishing to a healthy status. However, the exploitation status of high-trophic-level fish species, such as conger pike and groupers, were still in overfished status. Assessment based on length data was less optimistic. Our uncertainty analysis showed that the catch-based model is less sensitive to parameters compared with the two length-based models considered here. We advocate for more practical and precise fisheries management in China, such as category/species-based management, further optimization and improvement of the fishing structure, development of a scientific quota-based system, ecosystem management that incorporates climate factors, and establishment of marine protected areas for fish species that are severely overfished or have high ecological value.

The impact of global warming on fish distribution is a key factor in fishery management and sustainable development. However, limited knowledge exists regarding the influence of environmental factors on the distribution of Evynnis cardinalis under climate change. This study addresses this gap by predicting the species distribution under current conditions and three future climate scenarios (SSP126, SSP370, and SSP585) using five individual models and four ensemble models. The results demonstrate that the ensemble models outperform the single models, with majority voting (EMca) achieving the highest accuracy (ROC = 0.97, TSS = 0.85). Bathymetry (BM) and the sea surface height (SSH) are the primary factors influencing the distribution. The predictions indicate that the currently suitable habitats of E. cardinalis are primarily located in the Beibu Gulf region of the northern South China Sea. Under future climate scenarios, suitable habitat areas are expected to expand to higher latitudes and deeper waters, though highly suitable habitats in the western Guangdong coastal waters, western Beibu Gulf, and southwestern offshore waters of Hainan Island will significantly decrease.

For over 40 years, largehead hairtail Trichiurus japonicus have been the most economically significant fish in China. However, limited research on this species has occurred in the South China Sea, rendering the exploitation status of this resource in this region uncertain. We evaluate population dynamics and the status of largehead hairtail in the northern South China Sea to inform sustainable fisheries management. Using long-term data during 1981-2023, we apply three data-limited assessment methods: Length-Based Bayesian Biomass Estimation (LBB), Length-Based Spawning Potential Ratio (LBSPR), and the Monte Carlo Catch-Maximum Sustainable Yieldtype model (CMSY). The LBB analysis indicates that B/BMSY was 0.49 in 1981-1982, dropped to 0.11 in 2006-2007, and reached 0.35 in 2023. LBSPR results reveal an SPR value of 0.30 in 1981-1982, stabilizing at 0.03 from 1998-2020, and slightly increasing to 0.05 from 2021-2023. The CMSY model estimates a B/BMSY of 0.99 for 2023. All three assessment models consistently reveal the largehead hairtail population to have experienced overfishing. Various management measures have reduced overfishing in recent years, and these actions have positively impacted largehead hairtail stocks. However, further management is necessary to ensure largehead hairtail stock sustainability.